Version Compatibility

Reference examples tested with: liana 1.2+, CellChat 2.1+, cellphonedb 5.0+, nichenetr 2.1+, scanpy 1.10+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Cell-Cell Communication Analysis

"Find which cell types signal to each other" -> Score ligand-receptor pairs from co-expression in sender and receiver populations, rank them, and assess specificity or downstream effect.

• Python: liana.mt.rank_aggregate() (consensus default), cellphonedb (permutation specificity)
• R: CellChat::computeCommunProb() (pathway probability), nichenetr::predict_ligand_activities() (downstream mechanism)

Governing Principle